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Research: Convergent origination of a Drosophila-like dosage compensation mechanism in a reptile lineage
- Ray Marin,
- Diego Cortez,
- Francesco Lamanna,
- Madapura M. Pradeepa,
- Evgeny Leushkin,
- Philippe Julien,
- Angélica Liechti,
- Jean Halbert,
- Thoomke Brüning,
- Katharina Mössinger,
- Timo Trefzer,
- Christian Conrad,
- Halie N. Kerver,
- Juli Wade,
- Patrick Tschopp,
- and Henrik Kaessmann
Genome Res. December 2017 27: 1974-1987; Published in Advance November 13, 2017, doi:10.1101/gr.223727.117
...transcriptomic, genomic, and histone modification data for Anolis and representative tetrapod species (Fig. 1; Methods). For Anolis, we collected transcriptome data using high-throughput strand-specific RNA sequencing (RNA-seq) for 30 adult and 48 embryonic samples (covering most of prehatching development...
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Research: Comparative epigenomics in distantly related teleost species identifies conserved cis-regulatory nodes active during the vertebrate phylotypic period
- Juan J. Tena,
- Cristina González-Aguilera,
- Ana Fernández-Miñán,
- Javier Vázquez-Marín,
- Helena Parra-Acero,
- Joe W. Cross,
- Peter W.J. Rigby,
- Jaime J. Carvajal,
- Joachim Wittbrodt,
- José L. Gómez-Skarmeta,
- and Juan R. Martínez-Morales
Genome Res. July 2014 24: 1075-1085; Published in Advance April 7, 2014, doi:10.1101/gr.163915.113
...selected embryos within the pharyngula period for these two organisms (Irie andKuratani 2011). For Xenopus, previously published data from stage 24–26 embryos were included in our study (Tan et al. 2013). For mouse, we performed a complete RNA sequencing analysis in duplicate using 10.5-d embryos (Pearson...
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Resource: Coelacanth genomes reveal signatures for evolutionary transition from water to land
- Masato Nikaido,
- Hideki Noguchi,
- Hidenori Nishihara,
- Atsushi Toyoda,
- Yutaka Suzuki,
- Rei Kajitani,
- Hikoyu Suzuki,
- Miki Okuno,
- Mitsuto Aibara,
- Benjamin P. Ngatunga,
- Semvua I. Mzighani,
- Hassan W.J. Kalombo,
- Kawilarang W.A. Masengi,
- Josef Tuda,
- Sadao Nogami,
- Ryuichiro Maeda,
- Masamitsu Iwata,
- Yoshitaka Abe,
- Koji Fujimura,
- Masataka Okabe,
- Takanori Amano,
- Akiteru Maeno,
- Toshihiko Shiroishi,
- Takehiko Itoh,
- Sumio Sugano,
- Yuji Kohara,
- Asao Fujiyama,
- and Norihiro Okada
Genome Res. October 2013 23: 1740-1748; Published in Advance July 22, 2013, doi:10.1101/gr.158105.113
...- assembly was performed with the newly developed assembler PLATANUS, which is optimized for short-read data from high-throughput sequencers. See Supplemental Information 2.3 for details. Genome browser The Coelacanth Genome Browser has been established using the assembled sequence and RNA-seq data...
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Research: Fusion, fission, and scrambling of the bilaterian genome in Bryozoa
- Thomas D. Lewin,
- Isabel Jiah-Yih Liao,
- Mu-En Chen,
- John D.D. Bishop,
- Peter W.H. Holland,
- and Yi-Jyun Luo
Genome Res. January 2025 35: 78-92; Published in Advance January 6, 2025, doi:10.1101/gr.279636.124
...on different chromosomes using published RNA sequencing (RNA-seq) data (Supplemental Fig. S13; Supplemental Table S14). In C. mucedo, both the Hox4b and Lox5b genes separated from the main cluster are expressed more highly than their main cluster counterparts Hox4a and Lox5a (paired t-tests P = 0.0009 and P...
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Research: Widespread roles of enhancer-like transposable elements in cell identity and long-range genomic interactions
- Yaqiang Cao,
- Guoyu Chen,
- Gang Wu,
- Xiaoli Zhang,
- Joseph McDermott,
- Xingwei Chen,
- Chi Xu,
- Quanlong Jiang,
- Zhaoxiong Chen,
- Yingying Zeng,
- Daosheng Ai,
- Yi Huang,
- and Jing-Dong J. Han
Genome Res. January 2019 29: 40-52; Published in Advance November 19, 2018, doi:10.1101/gr.235747.118
...structure based on known lineage groups (cluster purity = 0.812, where cluster purity = 1.0 − [misaligned dendrites/total dendrites]) (Fig. 2C). A previous study has reported that NJT built using ±1.5 kb H3K4me1 densities of long-intergenic noncoding RNAs (lincRNAs) TSSs is the best lineage classification...
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